Monday, September 30, 2013

Down goes another barrier between humans and other animals. Researchers from the University of Zurich have found evidence that orangutans plan for the future.

There have been many examples of captive animals appearing to plan for the future. One famous example is of a chimpanzee who cached rocks ahead of time to throw at visitors (luckily, chimps have notoriously bad aim). The question the authors wished to address was whether wild animals can also lay plans. To answer it, they turned to the orangutans of Sumatra (Pongo abelii).

Male orangutans travel about a kilometer each day. About four times each day, mature male orangutans will face a particular direction and emit loud vocalizations known as ‘long calls’ that can last for up to four minutes. These calls identify the ‘speaker’, attract females and higher-ranking males, and repel lower-ranking males. After making these calls, the apes resume moving through the forest (unless it's the last call of the day, made from that evening's nest). As these calls are amplified in one direction, other orangutans can use that information to meet up with, or avoid, the caller. So, at the end of the day, do the male orangutans end up more or less where they said they would be? The following graphic illustrates two possible expected outcomes. If orangutans travel independently of the direction in which they’re shouting, the average deviation between the two would be 90° (left). If, on the other hand, the travel direction was not random, there would be considerably less than 90° between long call and travel direction (right).

When the data was analyzed, the researchers found that the long call direction did more or less predict the subsequent travel direction. At least, the deviation between those two directions was significantly less than 90°. In particular, males began their day by moving in the direction they had announced before retiring the previous night. At the very least, this indicates some ability to remember what they had planned to do the night before.

The graph depicts the median of deviation angles between travel direction and the direction of the last spontaneous long call of the previous day, given shortly before nesting or from the nest. Time is clock time during the day following the long call.

The authors conclude from this that the orangutans are indeed planning for the future. They decide on a direction of travel, announce where they intend to go, and then go there.

One counterargument is that the apes have to face in some direction during the long call, and they simply continue traveling in the direction they’re already facing. In other words, they aren’t really planning ahead, it’s just coincidence that the call direction and travel direction match up. However, keep in mind that we’re not talking about striding along a road. It’s impossible for a large animal to travel in a straight line through the trees of Sumatra. It’s not even clear what clues the animals could be using to navigate through the canopy. Yet, despite following a convoluted, meandering path, the orangutans still end up where they said they would be.

Friday, September 27, 2013

In Jurassic Park, scientists pull dinosaur DNA out of blood-sucking insects encased in amber that is millions of years old. University of Manchester scientists, led by David Penney, show just how implausible this intriguing idea is when they failed to extract insect DNA from 10,000 year old samples.

Certain types of trees produce thick gummy resin. Over time, the resin hardens, first into a product called ‘copal’, and then into the more familiar, and far more ancient, amber. It was from 10,000 year old copal that the entomologists tried to pull DNA. They pulverized two stingless bees embedded in the copal and, using the most stringent methodology to prevent contamination (sterilizing all surfaces and wearing forensic suits), attempted to extract DNA.

While they did get some DNA, none of it matched known stingless bee databases. The best sequence they got was a 452 nucleotide string from a bacterium. This is about half the length of an average bacterial gene. The authors are quick to defend their DNA extraction prowess, stating that they had had no trouble getting DNA from other samples.

To be clear, the researchers were not attempting to resurrect ancient vertebrates. As entomologists, they were primarily interested in collected the genomes of extinct or rare insects. However, it’s pretty clear that our hopes of ever visiting Jurassic Park are dashed. If you can’t get insect DNA out of an insect embedded in 10,000 year old copal, you aren’t going to be able to get dinosaur DNA from the blood meal of an insect embedded in 100 million year old amber.

Thursday, September 26, 2013

If you’re willing to spelunk deep inside a Croatian cave, you just might find a specimen of a newly discovered see-through snail dubbed Zospeum tholussum.

Zospeum tholussum, 2013.

Credit: Alexander M. Weigand

Alexander Weigand discovered the snail nearly a thousand meters below the surface in the Lukina Jama-Trojama cave system in the Velebit mountain range of Croatia. I’m not sure whether exploring this cave system would be more likely to give me vertigo, claustrophobia or acrophobia. But you can judge for yourself.

Wednesday, September 25, 2013

Entomologist Walter Tschinkel has turned ant colonies into works of art. Literally. He pours molten aluminum down the ant holes and then excavates the solidified ant hills.Here's one result:More pictures here. See how Tschinkel's makes his colony casts below:

Tuesday, September 24, 2013

You’ve heard of the genome, which is the set of all genes within a cell. In the same way, the ‘metabolome’ is the set of all small metabolites found within a sample. Thanks to the work of University of Alberta researchers led by Souhaila Bouatra, we’re closing in on the human urine metabolome. I know that was keeping you up at night.

Urine is surprising complex and medically relevant. Many diseases can be diagnosed by testing the levels of glucose, protein, nitrates or other molecules within urine, often with a simple dipstick test. You could hardly ask for a less invasive test. Therefore, the more comprehensive the list of all the components found in urine, together with the consequences for deviating from normal ranges, the better.

The authors were able to identify hundreds of unique metabolites within the urine samples using the following techniques:

I think it’s safe to say that the researchers were extremely thorough in their search for urine metabolites. Even though the urine metabalome should be a subset of the blood metabalome (everything in urine was originally pulled out of the bloodstream by the kidneys), the researchers found many compounds not previously found in blood. Most likely, these metabolites are present below the threshold of detection in blood but become highly concentrated in the urine.

You can see the complete list of all the urinary compounds identified, from this study and from a literature search, at the Urine Metabalome Database. If you’re so inclined, you can also browse through chemical structures, maps of metabolic pathways, or clinical data.

The authors offer this fun fact:

The average adult generates between 1.5–2.0 liters of urine per day, which over the course of their lifetime would be enough to fill a small backyard swimming pool (5 X 8 X 1.5 m).

Monday, September 23, 2013

So, some new guidelines on treating asthma have come out and you want to make sure your fellow hospital staff are up to date on the changes. You could pass around memos and emails and hope people will bother to read them. Or, you could follow the example of Tapas Mukherjee from Glenfield Hospital and sing about it.

Mukherjee presented his findings at the European Respiratory Society Annual Congress. Before his video appeared on social media sites, only 62% of the health care professionals at Glenfield Hospital had even heard of the new asthma guidelines. Two months later, 100% were aware of them. More importantly, asthma management had also improved during that time.Of course, the increased awareness might not have been due solely to the video. Hospital staff did have two more months to become acquainted with the new asthma treatment protocols through other means. However, I wouldn’t be surprised if at the very least, the song helped people remember to follow the guidelines. After all, it's so catchy.

(If this doesn't play directly, click the YouTube icon at the bottom right).

Friday, September 20, 2013

Who doesn’t love watching a cheetah chase down its prey? Their unprecedented speed allows them to run down anything in the animal kingdom. However, antelope don't flee in a straight line. It’s not enough to simply run full out when your prey is employing a quick turning strategy. Turning at high speed puts great strain on the cheetah’s limbs and muscles. A better strategy might be to quickly close the distance to the prey and then slow down to follow the prey through its turns. And that’s exactly what cheetahs do.An international team of scientists led by John Wilson of North Carolina State University put GPS and accelerometer loggers on six wild cheetahs in Kgalagadi Transfrontier Park in southern Africa. They logged information on 41 chases, none lasting more than a minute.

The cheetahs did not accelerate to top speed and maintain that speed until the prey was caught or the cheetah gave up. Instead, they accelerated to high speed but then slowed down to match the speed and turns of their prey. This means that, contrary to conventional wisdom, the cheetahs never ended up traveling faster than racehorses.But here’s what you really want to see. Slo-mo footage of a running cheetah. Enjoy.

If you want to see how this film was made, skip ahead to 5:40. And you can see the cheetah's actual running speed at about 6:10.

Thursday, September 19, 2013

Among patients with obsessive-compulsive disorder (OCD), a few also have schizophrenia. But how can you tell if a person is suffering only from OCD or if he also has schizophrenia? This question is not as trivial as it sounds. Many of the symptoms of OCD are also found in people with both disorders (schizo-OCD), yet sufferers of these conditions require different treatments.

As the name suggests, people with OCD are riddled with obsessions (thoughts, images or impulses they can’t get rid of) and compulsions (the necessity to perform specific, repetitive actions). Schizophrenics usually have delusions and hallucinations. However, many people with schizophrenia also have OCD and perform the same ritualistic actions that OCD sufferers do. Luckily, according to a study by David Eilam and his colleagues from Tel Aviv University, there are differences that can be used to distinguish OCD from schizo-OCD.

Take a look at the video below. It compares the behavior of an OCD patient (left) and a schizo-OCD patient (right) preparing to leave their apartments. While they each feel compelled to perform many ritualistic actions before they can exit, there’s much more traveling around by the schizo-OCD patient.

The locations of the black circles show where an action took place, and the size of the circle indicates how many times an action was repeated at that spot. The OCD patient stands in the same place repeating the same action (like checking for his keys) up to ten times. Once he’s satisfied, his path to the front door is direct. In contrast, the person who also has schizophrenia travels all around his apartment, switching lights on and off, checking possessions, etc. An observer would have no idea that his ultimate goal was to exit the apartment.

Doctors might be able to use these differences in behavior to distinguish OCD patients from schizo-OCD patients. This is important because patients with schizophrenia require different and often more intense treatment than OCD patients.Gershoni A, Hermesh H, Fineberg NA, & Eilam D (2013). Spatial behavior reflects the mental disorder in OCD patients with and without comorbid schizophrenia. CNS spectrums, 1-14 PMID: 23845600.

Tuesday, September 17, 2013

If you’re a fungus-growing ant patiently tending your garden, the last thing you want is to have your nest invaded by parasitic invader ants who make themselves at home by consuming your young. Unless those uninvited guests end up protecting you from other predator ants that are much worse. That’s the symbiotic relationship some host ants have reached with their parasites.

Let me introduce you to three kinds of ants. Sericomyrmexamabilis(the host ants, top) are farmers. Megalomyrmexsymmetochus(guests, middle) are parasites that invade the gardeners’ nests. Once there, they feast on both the host brood and on their fungus garden, but slowly enough so that the colony isn't obliterated. Megalomyrmex also trap the host queens within the colony by clipping their wings, ensuring a steady supply of ant baby fodder. In this way, the Megalomyrmex set themselves up as permanent guests. Finally, there are Gnamptogenys hartmani (raiders, bottom). These marauding predators completely take over any fungus gardens they find, driving out or killing all the host ants.

Rachelle Adams and her colleagues from the University of Copenhangen have found that while the host ants are ill equipped to drive away the raiders, their parasitic guests have more potent weaponry. Nests containing even a moderate number of these guest ants were completely protected from the raiding ants. Often raiding colonies will avoid nests with odors indicating the presence of the guest parasites.

Needless to say, this puts the poor host ants in a difficult position. They have to accept the constant culling of their young and their resources or face the likely extinction of the entire colony. Clearly, the former is the lesser of two evils. Of course, no one is asking them what they think, least of all the researchers, who staged caged death matches between different numbers and types of ants.

Monday, September 16, 2013

If you want a male partner who will share the parenting duties, you might want to choose someone with smaller testicles. So says a new study by Jennifer Mascaro, Patrick Hackett and James Rilling from Emory University. There’s a hypothesis within evolution that is referred to as the ‘life history theory’. Briefly, an organism only has a finite amount of energy to expend toward its ultimate goal: reproduction. A creature that grows an enormous reproductive display may attract more mates, but it will produce smaller litters. A mother can abandon a thousand babies to the ocean currents, but she can only nurture a handful at a time. Each strategy is a trade-off.

Human males also exhibit a range of parenting and mating strategies. To put it bluntly, how much of their energy do they spend trying to get the girl and how much caring for the resulting children? The answer may lie in their hormones and in their testicles. Males (human and other species) with high testosterone have greater mating success. However, they also spend less time caring for their offspring. The authors found that there is another, independent, correlation between nurturing and testicle size.In many species, testicle size is inversely proportional to the number of partners the females of the species are likely to mate with. That is, males from species where females are largely monogamous have small testes, whereas males from species where females have multiple partners have large testes. In case you’re wondering, among primates, humans have moderately sized testes. We’re socially monogamous but prone to cheating.There’s a part of the brain called the ‘ventral tegmental area’ (VTA). As part of the brain’s reward circuitry, the VTA is implicated in addiction, but also in strong emotional feelings, such as when one is holding one’s child.

Seventy fathers with small children were recruited for this study. Each man and his partner reported on his involvement in child caregiving, both actual and desired. The men had their testes volume and their testosterone levels measured. Finally, the researchers measured activity in the VTA while the men looked at pictures of their kids.

As expected, men with higher testosterone levels spent less time caring for their kids, and, perhaps more importantly, had no desire to spend more time with their kids. However, testes size also influenced how much fathers cared for their kids. Plus, according to activity recorded in the VTA, men with smaller testes felt more nurturing when viewing photos of their kids than did men with larger testes.

Obviously, this was a very small study (though perhaps we should be grateful that as many as 70 men allowed researchers to measure their testes). Still, it does align with life history theory. Men with high testosterone and/or large testes are better at mating but worse at parenting the resulting offspring.

Mascaro JS, Hackett PD, & Rilling JK (2013). Testicular volume is inversely correlated with nurturing-related brain activity in human fathers. Proceedings of the National Academy of Sciences of the United States of America PMID: 24019499.

Friday, September 13, 2013

Most of us have experienced a sunburn or two in our lives. But we don’t usually think about other animals getting sunburned. Especially not animals that spend the bulk of their lives under water. Apparently, as little time as whales are exposed to the sun is long enough for them to get sun damage. So say researchers led by Laura M. Martinez-Levasseur of the Zoological Society of London and Queen Mary University of London.

In humans, mitochondrial DNA (mtDNA) is a great biomarker for UV sun damage. MtDNA is both more easily damaged and less readily repaired than nuclear DNA. Thus, a lifetime of sun exposure can be seen in the accumulating mutations of skin mtDNA.

It’s also true in humans that darker skinned individuals (those with more melanin) suffer from less sun damage than lighter skinned individuals. Whales too come in different colors, though their differences tend to be species specific. Therefore, the authors used the three whale species shown below: blue whales, sperm whale and fin whales for their sunburn study.(A) From top to bottom:

For the light-skinned blue whales, the amount of sun damage, both in terms of visible lesions and mtDNA mutation levels was inversely proportional to the amount of melanin they had. That is, specimens that were a bit darker had less damage. Older whales had more lesions, suggesting that the damage was accumulating in the whales, just as it does in humans.

There are many factors involved in determining how much sun a whale is exposed to. Different whale species spend vastly different percentages of their time at the surface. Some species are highly migratory leading to seasonal differences in the intensity of the UV radiation they are subjected to. And of course, depletions in the ozone layer have led to increased skin damage in whales.

Luckily, there is some evidence that whales, like people, can acclimate to these changes by increasing the production of melanin. In other words, whales are able to tan.

Thursday, September 12, 2013

We’ve all made two personal observations about mosquitoes. First, we don’t like them, and for good reason. At best, mosquitoes are a minor irritation and at worst, they give you a deadly disease. For example, in Africa, the mosquito Anopheles gambiae is a major vector for malaria. Second, mosquitoes tend to come out in force as the sun is setting. Thanks to work by Samuel Rund and his colleagues from the University of Notre Dame, we now know why that might be. Mosquito feeding behavior is tied to the creatures’ circadian rhythms.

Circadian rhythms are internal biological patterns that follow a twenty-four hour period. For example, if you tend to get hungry to sleepy at about the same time of day regardless of what’s going on, you can thank your circadian clock. Virtually all living things have them, including plants and fungi.

For most organisms, these patterns of behavior are linked to the cycle of light and dark created by the sun. In the lab, scientists who work on circadian rhythms prefer to exert their own controls over what is considered ‘day’ or ‘night’. This is much more convenient than having to come in at odd hours to run experiments. Therefore, they train their test subjects to an artificial 24 hour pattern (made up of zeitgebers) that begins and ends at the time of the humans’ choosing. For the study organisms, this is no different from acclimating to a new time zone.

Once female A. gambiae mosquitoes (only females take blood meals) had successfully recovered from jet lag, the researchers pulverized the mosquitoes’ heads and extracted and quantified the proteins made in their antennae. In particular, the scientists were comparing the levels of odorant binding proteins (OBPs, molecules that bind to and transport signature odorant molecules) at different times of ‘day’.

It turns out that these OBPs wax and wane in expression throughout the day. The peak of protein abundance occurred four hours after lights-out, which would correspond to the middle of the night in the real world. However, it wasn’t just the light (or lack thereof) that was causing the spike in protein production. OBPs did not peak earlier in the day when mosquitoes were exposed to four hours of darkness in the middle of their ‘morning’. Thus, the daily rhythm of OBP expression is more deeply ingrained than simply following the position of the sun.

Flying and feeding behavior also peaked at about the same time as the OBPs, as determined by human volunteers sticking their arms into mosquito cages. Aren’t you glad you’re not a graduate student in that lab?

In summary, it’s not that mosquitoes are avoiding daytime predators (though they are also doing that) but that their prey-detecting senses are most acute at night. This makes bed nets for people in malaria hot spots all the more critical.Rund SS, Bonar NA, Champion MM, Ghazi JP, Houk CM, Leming MT, Syed Z, & Duffield GE (2013). Daily rhythms in antennal protein and olfactory sensitivity in the malaria mosquito Anopheles gambiae. Scientific reports, 3 PMID: 23986098.

Wednesday, September 11, 2013

Last week, NASA launched the Lunar Atmosphere and Dust Environment Explorer (LADEE). The craft will orbit the moon, gathering information on the lunar atmosphere. I didn't know there was any atmosphere on the moon either. However, there are a few more molecules near the moon's surface than out in space, so that counts by NASA's standards.

You can watch the launch below.

On this anniversary of the 9/11 attack, I think this gives us all a much more uplifting vision of humanity.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.